Skip to contents

Define a genetic component trait

Source: R/define_trait.R
define_trait.Rd

Creates one row in trait_meta describing a genetic component trait: a quantity with QTL effects in genome_effects, TBVs in ind_tbv, and additive genetic variance in trait_var_comp. Contains no phenotype-level information.

To register the observed phenotype that individuals receive records for, call define_phenotype() after this function. For the common one-off case use define_trait_simple(), which chains both steps together.

Usage

define_trait(
  pop,
  trait_name,
  target_add_var = NULL,
  target_add_mean = 0,
  expressed_parent = c("both", "parent_1", "parent_2"),
  description = NULL,
  units = NULL,
  overwrite = FALSE
)

Arguments

pop

A tidybreed_pop object.

trait_name

Character. Unique identifier for this genetic component trait. Must be a valid SQL identifier.

target_add_var

Numeric. Target additive genetic variance. Written to trait_var_comp as a diagonal entry under effect_name = "gen_add". Used by define_additive_effects() to rescale effects. If already set via define_effect_cov_matrix(), leave NULL.

target_add_mean

Numeric. TBV centering mean for the base population. Default 0; E[TBV] = 0 when TBVs are centered on base allele frequencies. The phenotypic population mean (intercept) is set separately in define_phenotype().

expressed_parent

Character. Parent-of-origin expression: "both" (default), "parent_1" (paternal), or "parent_2" (maternal). Imprinted traits use only the haplotype from the specified parent when computing TBVs.

description

Character. Free-text description of the trait.

units

Character. Measurement units, e.g. "kg", "count".

overwrite

Logical. If TRUE and a trait with the same name already exists, replace its trait_meta row and clear associated phenotype_effects rows. Default FALSE errors if the trait already exists.

Value

The modified tidybreed_pop (invisibly).

See also

define_phenotype(), define_additive_effects(), define_effect_fixed_class(), define_effect_fixed_cov(), define_effect_random(), add_phenotype(), define_trait_simple()

Examples

if (FALSE) { # \dontrun{
# Simple genetic component trait:
pop <- pop |>
  define_trait("ADG", target_add_var = 100, units = "g/day")

# Maternal component traits (no define_phenotype call needed for WWD/WWM):
pop <- pop |>
  define_trait("WWD", target_add_var = 200) |>
  define_trait("WWM", target_add_var = 80)

# Then define the observed composite phenotype:
pop <- pop |>
  define_phenotype("WW", type = "continuous", mean = 230,
    residual_var = 180,
    components = tibble::tribble(
      ~source_trait_name, ~contributor_type,
      "WWD", "self",
      "WWM", "dam"
    ))
} # }